6H7Y

X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with a inhibitor RNA 1-79-1


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829333% (v/v) pentaerythritol propoxylate PO/OH 5/4, 2 % (w/v) PEG 3350, 100 mM Tris-HCl, pH 8.0
Crystal Properties
Matthew coefficientSolvent content
3.3763.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.258α = 90
b = 131.376β = 90
c = 159.874γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90PIXELDECTRIS PILATUS3 2M2018-03-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.918BESSY14.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.815098.80.0730.0790.99916.176.796547-3-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.811.9293.40.8490.930.8711.946

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT3BI11.8147.2694359209998.670.150450.149830.17756RANDOM43.915
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
1.15-2.581.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.077
r_dihedral_angle_4_deg16.041
r_dihedral_angle_3_deg14.757
r_dihedral_angle_1_deg6.663
r_long_range_B_other5.442
r_long_range_B_refined5.442
r_scangle_other3.806
r_mcangle_it2.548
r_mcangle_other2.548
r_scbond_it2.507
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.077
r_dihedral_angle_4_deg16.041
r_dihedral_angle_3_deg14.757
r_dihedral_angle_1_deg6.663
r_long_range_B_other5.442
r_long_range_B_refined5.442
r_scangle_other3.806
r_mcangle_it2.548
r_mcangle_other2.548
r_scbond_it2.507
r_scbond_other2.507
r_mcbond_it1.824
r_mcbond_other1.824
r_angle_refined_deg1.802
r_angle_other_deg1.357
r_chiral_restr0.112
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_bond_other_d0.003
r_gen_planes_other0.002
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_scangle_it
r_metal_ion_refined
r_metal_ion_other
r_sphericity_bonded
r_rigid_bond_restr
r_sphericity_free
r_symmetry_vdw_refined
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5546
Nucleic Acid Atoms
Solvent Atoms427
Heterogen Atoms321

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing
Cootmodel building